Variant report

Variant	rs59000092
Chromosome Location	chr15:41626148-41626149
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr15:41626078-41626230	K562	blood:	n/a	n/a
2	POLR2A	chr15:41624146-41626151	Hela-S3	cervix:	n/a	n/a
3	IRF1	chr15:41626066-41626246	K562	blood:	n/a	n/a
4	HEY1	chr15:41624094-41626200	K562	blood:	n/a	n/a
5	POLR2A	chr15:41624014-41626233	Hela-S3	cervix:	n/a	n/a
6	ZNF384	chr15:41626130-41626228	K562	blood:	n/a	n/a
7	NFIC	chr15:41624539-41626322	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr15:41625879-41626205	GM12878	blood:	n/a	n/a
9	CHD1	chr15:41624239-41626294	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:41623974-41626186	SK-N-MC	brain:	n/a	n/a
11	CTCF	chr15:41626060-41626210	GM06990	blood:	n/a	n/a
12	TBL1XR1	chr15:41626128-41626263	K562	blood:	n/a	n/a
13	GTF3C2	chr15:41625093-41627178	Hela-S3	cervix:	n/a	n/a
14	RPC155	chr15:41625640-41626874	Hela-S3	cervix:	n/a	n/a
15	RUNX3	chr15:41625974-41626384	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:41625773-41626177	HL-60	blood:	n/a	n/a
17	MXI1	chr15:41623812-41626403	SK-N-SH	brain:	n/a	n/a
18	TBP	chr15:41624103-41626185	K562	blood:	n/a	n/a
19	STAT3	chr15:41626085-41626179	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr15:41626013-41626163	K562	blood:	n/a	n/a
21	RAD21	chr15:41624000-41626257	SK-N-SH	brain:	n/a	chr15:41624358-41624377

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41406745..41409392-chr15:41623521..41626579,5	K562	blood:
2	chr15:41625051..41627000-chr15:41692954..41695637,2	K562	blood:
3	chr15:41573497..41577986-chr15:41624362..41627823,9	K562	blood:
4	chr15:41624382..41626552-chr15:41708725..41711080,3	K562	blood:
5	chr15:41575115..41577125-chr15:41624466..41626801,3	MCF-7	breast:
6	chr15:41314841..41316914-chr15:41624845..41626746,2	K562	blood:
7	chr15:41624254..41626833-chr15:41952098..41954867,2	K562	blood:
8	chr15:41575029..41577348-chr15:41624329..41626974,5	K562	blood:
9	chr15:41624767..41626294-chr15:41694606..41696147,2	MCF-7	breast:

No data

Variant related genes	Relation type
OIP5	TF binding region
ENSG00000128908	Chromatin interaction
ENSG00000137815	Chromatin interaction
ENSG00000259521	Chromatin interaction
ENSG00000174197	Chromatin interaction
ENSG00000247556	Chromatin interaction
ENSG00000137806	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10518717	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851403	1.00[ASN][1000 genomes]
rs11070328	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1132639	0.83[EUR][1000 genomes]
rs11629979	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630656	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630799	1.00[ASN][1000 genomes]
rs11635269	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635565	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635906	1.00[ASN][1000 genomes]
rs11854081	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854632	1.00[ASN][1000 genomes]
rs11854820	1.00[ASN][1000 genomes]
rs11858068	1.00[ASN][1000 genomes]
rs11858812	1.00[ASN][1000 genomes]
rs13313520	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329235	1.00[ASN][1000 genomes]
rs13329579	1.00[ASN][1000 genomes]
rs1757468	1.00[ASN][1000 genomes]
rs17730589	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17730888	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866399	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899	1.00[ASN][1000 genomes]
rs2118740	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2448402	1.00[ASN][1000 genomes]
rs2730056	1.00[ASN][1000 genomes]
rs2730058	1.00[ASN][1000 genomes]
rs28377562	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382348	1.00[ASN][1000 genomes]
rs28416360	1.00[ASN][1000 genomes]
rs28421136	1.00[ASN][1000 genomes]
rs28437576	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448670	0.87[EUR][1000 genomes]
rs28456082	1.00[ASN][1000 genomes]
rs28458941	1.00[ASN][1000 genomes]
rs28463309	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28477406	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492932	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493087	1.00[ASN][1000 genomes]
rs28493702	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535540	1.00[ASN][1000 genomes]
rs28555198	1.00[ASN][1000 genomes]
rs28557159	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28576457	1.00[ASN][1000 genomes]
rs28584379	1.00[ASN][1000 genomes]
rs28617619	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28623183	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28661013	1.00[ASN][1000 genomes]
rs28663426	1.00[ASN][1000 genomes]
rs28673484	1.00[ASN][1000 genomes]
rs28687846	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28700583	1.00[ASN][1000 genomes]
rs28703570	1.00[ASN][1000 genomes]
rs28712264	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28716689	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28827035	1.00[ASN][1000 genomes]
rs28897479	1.00[ASN][1000 genomes]
rs316604	1.00[ASN][1000 genomes]
rs316606	1.00[ASN][1000 genomes]
rs316607	1.00[ASN][1000 genomes]
rs316611	1.00[ASN][1000 genomes]
rs316616	1.00[ASN][1000 genomes]
rs3204853	1.00[ASN][1000 genomes]
rs34665396	1.00[ASN][1000 genomes]
rs513280	1.00[ASN][1000 genomes]
rs521890	1.00[ASN][1000 genomes]
rs522063	1.00[ASN][1000 genomes]
rs55725658	1.00[ASN][1000 genomes]
rs56341337	0.85[EUR][1000 genomes]
rs56400990	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493000	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493003	1.00[ASN][1000 genomes]
rs691011	1.00[ASN][1000 genomes]
rs691906	1.00[ASN][1000 genomes]
rs691907	1.00[ASN][1000 genomes]
rs7162231	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163989	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164211	1.00[ASN][1000 genomes]
rs7164684	1.00[ASN][1000 genomes]
rs7165396	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165914	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167706	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168002	1.00[ASN][1000 genomes]
rs7168307	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168431	1.00[ASN][1000 genomes]
rs7169543	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181982	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182324	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72737786	1.00[ASN][1000 genomes]
rs72737792	1.00[ASN][1000 genomes]
rs72737793	1.00[ASN][1000 genomes]
rs72739630	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72739644	1.00[ASN][1000 genomes]
rs8023530	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030228	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8034840	1.00[ASN][1000 genomes]
rs8036026	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8036734	1.00[ASN][1000 genomes]
rs8037574	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038132	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8038983	1.00[ASN][1000 genomes]
rs8041809	1.00[ASN][1000 genomes]
rs8043237	1.00[ASN][1000 genomes]
rs9568	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044438	chr15:41560160-41745480	Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv1038923	chr15:41585028-41754890	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1045142	chr15:41585044-41738314	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv1039283	chr15:41620499-41745480	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs59000092	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs59000092	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs59000092	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs59000092	NDUFAF1	cis	Thyroid	GTEx
rs59000092	OIP5-AS1	cis	Artery Tibial	GTEx
rs59000092	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs59000092	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs59000092	OIP5-AS1	cis	Nerve Tibial	GTEx
rs59000092	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs59000092	NDUFAF1	cis	Muscle Skeletal	GTEx
rs59000092	NDUFAF1	cis	multi-tissue	Pritchard
rs59000092	OIP5-AS1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41623000-41626800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr15:41623000-41627200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr15:41623000-41627200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr15:41623000-41627200	Active TSS	A549	lung
5	chr15:41623000-41627400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:41623400-41627000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:41623400-41627200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr15:41623400-41627200	Active TSS	H1 Cell Line	embryonic stem cell
9	chr15:41623400-41627400	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr15:41623600-41626800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:41623600-41626800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:41623600-41626800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:41623600-41627000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:41623600-41627000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr15:41623600-41627200	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr15:41623600-41627200	Active TSS	Thymus	Thymus
17	chr15:41623600-41627200	Active TSS	Hela-S3	cervix
18	chr15:41623800-41626200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:41623800-41626200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:41623800-41626400	Active TSS	Osteobl	bone
21	chr15:41623800-41626600	Active TSS	Fetal Thymus	thymus
22	chr15:41623800-41626800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:41623800-41627200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:41623800-41627200	Active TSS	NHDF-Ad	bronchial
25	chr15:41623800-41627400	Active TSS	GM12878-XiMat	blood
26	chr15:41623800-41627400	Active TSS	K562	blood
27	chr15:41624000-41626200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:41624000-41626200	Active TSS	Esophagus	oesophagus
29	chr15:41624000-41626200	Active TSS	HMEC	breast
30	chr15:41624000-41626600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:41624000-41626600	Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr15:41624000-41626600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:41624000-41626600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:41624000-41626600	Active TSS	NHEK	skin
35	chr15:41624000-41626800	Active TSS	Fetal Intestine Small	intestine
36	chr15:41624000-41627200	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr15:41624000-41627400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr15:41624200-41626200	Active TSS	Fetal Intestine Large	intestine
39	chr15:41624200-41626200	Active TSS	Stomach Mucosa	stomach
40	chr15:41624200-41626400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:41624200-41626400	Active TSS	Dnd41	blood
42	chr15:41624200-41626600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr15:41624200-41626600	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr15:41624200-41626800	Active TSS	Fetal Kidney	kidney
45	chr15:41624200-41626800	Active TSS	NHLF	lung
46	chr15:41624200-41627000	Active TSS	Fetal Lung	lung
47	chr15:41624200-41627200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:41624200-41627200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:41624200-41627200	Active TSS	HSMM	muscle
50	chr15:41624200-41627400	Active TSS	Muscle Satellite Cultured Cells	--

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